Using scripts in VMD

how to execute a script

scripts can be a list of instructions

in the vmd console type "play script"

or they can contain procedures

in the vmd console type "source script" then "procedure name"

scripts are written in Tcl
a good web-page for Tcl link
VMD has some of its own language
the script has to be in the directory you execute from

a simple script to load and define the representation for a molecule

the following will explain this basic script Basic_script.txt

it is best to first set the display settings

set the background colour

all atoms same size=orthographic depth=perspective

turn off the depth shading

turn off the axes

color Display Background iceblue
display projection   Orthographic
display nearclip set 0.000000
display farclip  set 10.000000
display depthcue   off
axes location off

reading in the structure

VMD will read a .xyz file of the following format:

number of atoms

title

atom x y z

where atom=atomic_symbol or atom=atomic_number

using the GUI => file:new molecule

using a script

# read in new molecule
mol new mol.xyz type xyz

the first representation on loading is always lines

delete the top representation

mol delrep 0 top

for a standard CPK representation on everything

CPK is VDW and bonds

the order of the next arguments is important

sphere_scale bond_radius sphere_resoluyion bond_resolution

select how colours are determined in this case via atomic name

we want opaque atoms as the material

apply the changes

mol selection {all}
mol representation CPK 1.100000 0.300000 20.000000 16.000000
mol color Name
mol material Opaque
mol add rep top

set specific atom colours and sizes

do this by changing colour redrawing the item

must do it for each item individually

must also respecify CPK to make the bonds the right colour

this is only added OVER the existing representation

all items will be this colour until the colour is changed again

colorID0=blue

colorID1=red

colorID2=grey

colorID7=green

colorID8=white

mol selection {name C}
mol representation CPK 1.100000 0.300000 20.000000 16.000000
mol color ColorID 2
mol addrep top

changing VDW defaults slightly to draw larger atom

VDW arguments are radius_size vdw_resolution

mol selection {name C}
mol color ColorID 2
mol representation VDW 0.3 30.0
mol addrep top

changing bond defaults slightly to draw fatter bonds

problem is that this only changes X-X bonds for atom X and not any others

so some of the bonds won't change colour properly

BOND arguments are bond_size bond_resolution

mol selection {name C}
mol color ColorID 2
mol representation bonds 0.3 16.0
mol add rep top

a simple script to load and define the representation for a trajectory

the following will explain this basic script Basic_traj_script.txt

load a trajectory

# read in trajectory
mol new traj.xyz type xyz

CPK does not always work because of bonds across the cell

so we add dynamic bonds and make all the atoms VDW

for example to make the Oxygen red and Hydrogen white

#dynamic bonds
 mol selupdate 0 0 1
 mol representation DynamicBonds 1.4 0.1 6.0
 mol color Name
 mol material Opaque
 mol addrep top
# make water oxygen red
mol selection {name O}
mol color ColorID 1
mol representation VDW 0.20 30.0
mol addrep top
# make water hydrogen white
mol selection {name H}
mol color ColorID 8
mol representation VDW 0.20 30.0
mol add rep top

To add H-bonds:

add the HBonds representation with the following arguments

distance cut-off, angle cut-off, line thickness

here the bonds are coloured white (rather than the default red)

# add in H-bonds
mol selection {all}
mol color ColorID 8
mol representation HBonds 3.0 30.0 3.0
mol add rep top

Choose an individual molecule and change its representation

selecting a molecule does not work, so you have to do it by atom index

you will need to change the index numbers to those for your molecule

click on the Mouse:Query in the menu and then on the molecule screen, click on the atom

then look on the VMD terminal window, a list will appear relating to that atom and this will list the index no of the atom

in this case I have made one water molecule blue and enlarged the VDW spheres to make it stand out

mol selection {index 42 44 43}
mol color ColorID 0
mol representation VDW 0.5 30.0
mol add rep top